7B4O

A Bacteroidetes bacterium CuZn-superoxide dismutase with ZnZn metalation

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2C9V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	295	100 mM tris(hydroxymethyl)aminomethane-HCl, 20 % polyethylene glycol 6000, 2 mM ZnCl2

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.469	α = 90
b = 96.637	β = 90
c = 136.118	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M		2020-09-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.9786	SOLEIL	PROXIMA 1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.41	68.27	100	0.998	10.2	7.5		122059

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.41	1.43			0.345

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2c9v	1.41	68.27	122006	6227	99.974	0.161	0.1589	0.1918	19.872

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
2.371			-3.167		0.795

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.22
r_dihedral_angle_4_deg	19.742
r_dihedral_angle_3_deg	11.244
r_scangle_it	9.102
r_scangle_other	9.102
r_rigid_bond_restr	8.217
r_scbond_it	7.662
r_scbond_other	7.661
r_dihedral_angle_1_deg	6.868
r_lrange_it	6.688
r_lrange_other	6.558
r_mcangle_it	2.101
r_mcangle_other	2.101
r_mcbond_it	1.534
r_mcbond_other	1.534
r_angle_other_deg	1.384
r_angle_refined_deg	1.358
r_nbd_other	0.228
r_symmetry_nbd_refined	0.214
r_nbd_refined	0.187
r_symmetry_nbd_other	0.18
r_symmetry_metal_ion_refined	0.169
r_xyhbond_nbd_refined	0.151
r_nbtor_refined	0.147
r_symmetry_xyhbond_nbd_refined	0.118
r_ncsr_local_group_2	0.099
r_ncsr_local_group_6	0.097
r_ncsr_local_group_1	0.092
r_ncsr_local_group_5	0.085
r_metal_ion_refined	0.078
r_symmetry_nbtor_other	0.075
r_ncsr_local_group_3	0.063
r_chiral_restr	0.062
r_ncsr_local_group_4	0.05
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4440
Nucleic Acid Atoms
Solvent Atoms	564
Heterogen Atoms	15

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data reduction
Aimless	data scaling
MOLREP	phasing